AMBER Archive (2004)

Subject: Re: AMBER: about FEP

From: david.evans_at_ulsop.ac.uk
Date: Tue Nov 02 2004 - 05:28:44 CST

Hi,

Have you set up your prmtop file with the correct information for the
perturbation? I.e. in leap input commands like (randomly pulled from
one of my systems, read the manual for yours)

set complex.90.C2 pert true
set complex.90.C2 pertName N1
set complex.90.C2 pertType nd
set complex.90.C2 pertCharge -0.0693
.....
saveAmberParmPert complex prmtop prmcrd

The first "pert true" command is missing (I think) from the Amber8
manual, but seems to be necessary.

Dave Evans
London School of Pharmacy

---- Message from Annette Ho"glund
<hoeglund_at_informatik.uni-tuebingen.de> at 2004-11-02 11:44:03 ------
>Dear All,
>
>I have been experiencing the same thing (zeros everywhere and no free
>energy is collected) when trying to perform TI using sander. I
perform
>minimization and equilibration (as I would do for a simulation)
before
>the TI step.
>Could someone help and perhaps post an input for sander TI (and
perhaps
>also the min and equil input before that) applicable to a protein?
>
>Regards,
>Annette
>
>
>Xiao He wrote:
>
>>Dear Amber users,
>> I want to use thermodynamic free energy calculations,
>>
>>I read the manual and try a system like this
>>
>> nstlim=1000,ntpr=100
>> icfe=1,
>> clambda=0.5,
>> klambda=4,
>> ntb=0,
>> temp0 = 300.0, tautp = 1.0,
>> ntf = 2, ntc = 2,
>> dt = 0.002,
>> ntave = 25,
>>
>>But it seems it does not calculate the free energy.
>>
>> DV/DL, AVERAGES OVER 25 STEPS
>>
>>
>> NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 0.00 PRESS =
  0.0
>> Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
>> BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
>> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
>> EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
>>
>>Would anyone like to tell me how to do it properly?
>>Thanks for your reply.
>>
>>Best wishes,
>>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Xiao He
>>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡hx_at_itcc.nju.edu.cn
>>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-11-02
>>
>>
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